It wasn't shunned but the game followed on the tail of the sack of lies that was 'ALIENS: Colonial Marines'. There was no confidence after that piece of shit was released. What made things worse was Pitchford's constant hyping of the Gearbox title promising everyone it was exactly what we wanted. It was hyped and hyped and hyped. When it was revealed to be a z-grade game most people became very wary of any games set within this property. ...and rightly so.
Also keep in mind, after 2 mediocre to poor 'AvP' movies and the 2010 'AvP' game was average at best, the series was tiring severely. 'A:CM' was almost the final nail in the coffin in terms of games in this series.
If 'ALIEN: Isolation' wasn't in production well before 'A:CM' was released, it would never have seen the light of day. It's only because SEGA had the licence to commit multiple studios to work on different Projects that it was given a chance of success.
After all, there's been no announcement or rumor for any AAA 'ALIEN' titles since then and it's been 3 years since 'ALIEN: Isolation' was released.